15 research outputs found
A new time-dependent density-functional method for molecular plasmonics: Formalism, implementation, and the Au144(SH)60 case study
We describe the implementation and application of a recently developed time-dependent density-functional theory (TDDFT) algorithm based on the complex dynamical polarizability to calculate the photoabsorption spectrum of large metal clusters, with specific attention to the field of molecular plasmonics. The linear response TDDFT equations are solved in the space of the density fitting functions, so the problem is recast as an inhomogeneous system of linear equations whose resolution needs a numerical effort comparable to that of a SCF procedure. The construction of the matrix representation of the dielectric susceptibility is very efficient and is based on the discretization of the excitation energy, so such matrix is easily obtained at each photon energy value as a linear combination of constant matrix and energy-dependent coefficients. The code is interfaced to the Amsterdam Density Functional (ADF) program and is fully parallelized with standard message passing interface. Finally, an illustrative application of the method to the photoabsorption of the Au144(SH)60 cluster is presented
Crystal Structure and Theoretical Analysis of Green Gold Au30(S-tBu)18 Nanomolecules and Their Relation to Au30S(S-tBu)18
We report the complete X-ray crystallographic structure as determined through single-crystal X-ray diffraction and a thorough theoretical analysis of the green gold Au30(S-tBu)18.
While the structure of Au30S(S-tBu)18 with 19 sulfur atoms has been reported, the crystal structure of Au30(S-tBu)18 without the \u3bc3-sulfur has remained elusive until now, though matrix-assisted laser desorption ionization mass spectrometry (MALDI-MS) and electrospray ionization mass spectrometry (ESI-MS) data unequivocally show its presence in abundance. The Au30(S-tBu)18 nanomolecule not only is distinct in its crystal structure but also has unique temperature-dependent optical properties. Structure determination allows a rigorous comparison and an excellent agreement with theoretical predictions of structure, stability, and optical response
Computational models of photosensitizers to be used in photodynamic therapy: from assisted delivery to light activation
Tesis Doctoral inédita cotutelada por la Universität de Wien y la Universidad Autónoma de Madrid, Facultad de Ciencias, Departamento de Química. Fecha de Lectura 25-02-2019Esta tesis tiene embargado el acceso al texto completo hasta el 25-08-2020Photodynamic therapy is an established treatment against certain types of cancer. This therapy
exploits the excited-state reaction of a photosensitizer (PS) with molecular oxygen and/or
biomolecules of the cells, after being irradiated with light, resulting in singlet oxygen or other
cytotoxic species. The success of this therapy is determined by the double selectivity achievable
thanks to the chemical and photophysical properties of the PS, which regulate the selective
accumulation in the tumour cells and the production of cytotoxic species, respectively. In
this thesis, theoretical modelling has been used to help the design of novel PSs and provide
useful insights into chemical problems related to the development of more efficient photodrugs.
In the first part of this thesis, BODIPYs were selected as a promising class of novel PS
for photodynamic therapy. BODIPYs show many of the desired chemical properties of PSs
but, often, their photophysics is not suited for efficient therapeutic effects. The absorption
maximum of the unsubstituted BODIPY is blue-shifted with respect to the energetic region
adequate to treat deep tumours. Moreover, its strong fluorescence indicates poor intersystem
crossing probabilities and thereby small triplet quantum yields, fundamental to produce cytotoxic
species. Here, two computational methods, CASPT2 and ADC(2), have been used to explore the
excited states topology of this dye. That study provided a detailed photophysical mechanism
of the bare BODIPY and determined the accuracy of ADC(2) against CASPT2, which was
used as reference, to investigate this family of dyes. Since the parent compound is unsuited
for photodynamic therapy applications, meso-substituted BODIPYs carrying halogen atoms have
been also investigated in close cooperation with biolitec research GmbH. It was found that
conjugated substituents in the meso position shift the absorption maximum to the red; however,
they also open a detrimental non-radiative deactivation channel to the ground state mediated
by a S1=S0-conical intersection that prevents efficient intersystem crossing. The introduction of
heavy atoms increases the intersystem crossing probabilities but lowers the relative energies of the
S1=S0-conical intersection, favouring internal conversion to the ground state. As a compromise,
a mono-brominated meso-ethyl-BODIPY was selected as best choice to perform non-adiabatic
molecular dynamics simulations with the SHARC method. Those calculations complemented the
stationary calculations and delivered the actual pathways to populate the triplet manifold and the
associated timescales. In the second part of the thesis, the emphasis was put on existing successful
photodrugs. Temoporfin is a second-generation PS but is very hydrophobic and presents several
issues when administrated to patients. For this reason, an assisted delivery using a liposome carrier
is currently being developed to deliver the PS more selectively to the targeted cells and provide
a more advantageous distribution of the PS inside them. Here, molecular dynamics simulations
were employed to unveil that the origin of the good loading capacity of the vesicles lies on the
formation of hydrogen bonds between Temoporfin and the carrier material. Furthermore, the
umbrella sampling technique was used to simulate the slow drug delivery process from the liposome
to a cell membrane and obtain a free-energy profile. The induced rigidity in the system at the
transient structure, again due to the formation of hydrogen bonds, explains the origin of the energy
barrier, which is then of entropic nature. Finally, at the conformation corresponding to the free
energy minimum, the excited states of the photodrug embedded in the hydrophobic environment
were calculated using QM/MM calculations.La terapia fotodinámica es un tratamiento establecido contra específicos tipos de cancer. Esta
terapia explota la reacción en el estado excitado de un compuesto fotosensible (PS) con oxígeno
molecular y/o biomoléculas celulares después de ser irradiado con luz, resultando en oxígeno singlete
u otras especies citotóxicas. El éxito de esta terapia es determinado por la doble selectividad que
se consigue gracias a las propiedades químicas y fotofísicas del PS, que regulan respectivamente
la acumulacion selectiva en las células tumorales y la producíon de especies citotóxicas. En esta
tesis han sido usados modelos teóricos para diseñar nuevos PSs y proporcionar perspectivas útiles
sobre problemas químicos relacionados con el desarrollo de foto-medicamentos mas eficientes. En
la primera parte de esta tesis, seleccionamos BODIPYs (usados generalmente como tintes) como
una clase prometedora de nuevos PS para ser usados en terapia fotodinámica. Los BODIPYs
presentan muchas de las propiedades químicas que deseamos que presenten los PS pero sus
propiedades fotofísicas generalmente no son adecuadas para efectos terapeuticos que sean eficientes.
El máximo de absorción del espectro visible del BODIPY más sencillo está desplazado al azul con
respecto de la region energética adecuada para tratar los tumores mas internos. Ademas su fuerte
fluorescencia indica una baja probabilidad de cruce entre sistemas y por lo tanto rendimientos
cuánticos de triplete bajos, que son fundamentales para producir especies citotóxicas. En este
estudio hemos usado dos métodos computacionales CASPT2 y ADC(2) para explorar la topologia
de los estados excitados de este tinte. Ese estudio proporcionó un mecanismo fotofísico detallado
del BODIPY más simple y determinó la exactitud de ADC(2) frente a CASPT2, que fue usado
como referencia para investigar esta familia de tintes. Como el compuesto base no es adecuado
para aplicaciones en terapia fotodinámica, también estudiamos BODIPY meso substituidos que
llevan además átomos de halógeno, en cooperación con la empresa biolitec research GmbH. Se
descubrió que substituyentes conjugados en posición meso desplazan hacia el rojo el maximo de
absorción; sin embargo también abren un indeseado canal de desactivación no radiativo hacia
el estado fundamental mediado por una intersección conica S1=S0 que previene un eficiente cruce
entre sistemas. La introducción de átomos pesados aumenta la probabilidad de cruce entre sistemas
pero disminuye la energía relativa de la interseccíon conica, favoreciendo la conversión interna al
estado fundamental. Para llegar a un compromiso, un meso-etil-BODIPY mono-brominado fue
seleccionado como el más cualificado para llevar a cabo simulaciones de dinámica molecular no
adiabática con el metodo SHARC. Este proceso complementó los calculos estáticos y produjo las
rutas más probables para poblar los estados tripletes y los tiempos de reaccíon asociados. En la
segunda parte de la tesis, pusimos enfasis en fotomedicamentos existentes que ya han sido utilizados
con éxito. Las Temoporfirinas son fotosensibilizadores de segunda generacion muy hidrofobicos
que presentan problemas cuando son administrados a pacientes. Por este motivo biolitec research
GmbH ha desarrolado una entrega asistida usando un liposoma como portador para poder llevar el
fotosensibilizador de un modo más selectivo a las células objetivo y proporcionar una distribución
más ventajosa del PS en su interior. En este punto utilizamos simulaciones de dinámica molecular
para descubrir que el origen de la gran capacidad de carga de las vesículas proviene de la formación
de enlaces de hidrógeno entre el Temoporfin y el material de transporte. Adicionalmente utilizamos
el metodo umbrella sampling para simular el lento proceso de transporte desde el liposoma a la
membrana celular y obtener así un perfil de energía libre. La rigidez inducida en el sistema en la
estructura transitoria, de nuevo debido a la formación de enlaces de hidrógeno, explica el origen
de la barrera energetíca, que es de naturaleza entrópica. Finalmente, en la conformación que
corresponde al mínimo de energía, los estados excitados del fotomedicamento rodeado por el medio
hidrofóbico fueron calculados usando QM/MM
Insight into the optical properties of meso-pentafluorophenyl(PFP)-BODIPY: An attractive platform for functionalization of BODIPY dyes
The pentafluorophenyl (PFP) moiety is an important and versatile substituent in the chemistry of BODIPYs, porphyrins and corroles. The widespread use of PFP meso-substituted compounds, as intermediates in the synthesis of more complex pyrrole derivatives, is the motivation behind this work, which investigates the optical properties of the meso-PFP-BODIPY from a theoretical point of view. From the panoply of computational tools available for this purpose, we have considered the MS-CASPT2//CASSCF multiconfigurational protocol, and other monoreference methods, including time dependent density functional theory, TD-DFT, the second order approximate couple cluster, CC2, and the algebraic diagrammatic construction scheme of the polarization propagator in its second order, ADC(2). We have identified ADC(2) as the most suited method for the characterization of the absorption properties of BODIPYs. Besides its computational efficiency and the small dependence shown towards the basis set flexibility, the results obtained with this method are independent from the preexisting knowledge of the system and its properties to be calculated by the user. In general, all the methods evaluated show a good performance when compared with experimental results, especially if implicit solvent effects are taken into account, delivering errors which amount to 0.05 eV. Finally, we discuss the effect of the electron-withdrawing PFP substituent at the meso-position on the absorption and emission energies of the boron-dipyrromethene core. The comparison of the PFP-substituted and core BODIPY spectroscopic properties reveals that this substituent red-shifts both the absorption and the emission of the parent dye. On the one hand, the incorporation of this substituent was found to reduce the HOMO-LUMO gap, and on the other it induces a strong destabilization of the electronic ground state along the global coordinate leading the system from the Franck-Condon region to the position of the first excited state, S1, minimum, suggesting a lower S1/S0 internal conversion funnel compared to the parent BODIPY compound.This work has been supported by the Project CTQ2015-63997- C2 of the Ministerio de Economía y Competitividad of Spain. I.C. gratefully acknowledges the “Ramón y Cajal” program of the Ministerio de Economía y Competitividad of Spain. M.D.V. thanks the Marie Curie Actions, within the Innovative Training Network-European Join Doctorate in Theoretical Chemistry and Computational Modelling TCCM-ITN-EJD-642294, for financial suppor
Solvent effects on electronically excited states: QM/Continuum versus QM/Explicit models
The inclusion of solvent effects in the calculation of excited states is vital to obtain reliable absorption spectra and density of states of solvated chromophores. Here we analyze the performance of three classical approaches to describe aqueous solvent in the calculation of the absorption spectra and density of states of pyridine, tropone, and tropothione. Specifically, we compare the results obtained from quantum mechanics/polarizable continuum model (QM/PCM) versus quantum mechanics/molecular mechanics (QM/MM) in its electrostatic-embedding (QM/MMee) and polarizable-embedding (QM/MMpol) fashions, against full-QM computations, in which the solvent is described at the same level of theory as the chromophore. We show that QM/PCM provides very accurate results describing the excitation energies of ππ∗ and nπ∗ transitions, the last ones dominated by strong hydrogen-bonding effects, for the three chromophores. The QM/MMee approach also performs very well for both types of electronic transitions, although the description of the ππ∗ ones is slightly worse than that obtained from QM/PCM. The QM/MMpol approach performs as well as QM/PCM for describing the energy of ππ∗ states, but it is not able to provide a satisfactory description of hydrogen-bonding effects on the nπ∗ states of pyridine and tropone. The relative intensity of the absorption bands is better accounted for by the explicit-solvent models than by the continuum-solvent approach.LG and JJN further acknowledge the University of Vienna for financial support, while MDV and MFSJM thank the Marie Curie Actions, within the Innovative Training Network-European Join Doctorate in Theoretical Chemistry and Computational Modelling TCCM-ITN-EJD-642294, for their respective PhD grant
Assessing Configurational Sampling in the Quantum Mechanics/Molecular Mechanics Calculation of Temoporfin Absorption Spectrum and Triplet Density of States
The absorption properties of Temoporfin, a second-generation photosensitizer employed in photodynamic therapy, are calculated with an electrostatic-embedding quantum mechanics/molecular mechanics (QM/MM) scheme in methanol. The suitability of several ensembles of geometries generated by different sampling techniques, namely classical-molecular-dynamics (MD) and QM/MM-MD thermal sampling, Wigner quantum sampling and a hybrid protocol, which combines the thermal and quantum approaches, is assessed. It is found that a QM description of the chromophore during the sampling is needed in order to achieve a good agreement with respect to the experimental spectrum. Such a good agreement is obtained with both QM/MM-MD and Wigner samplings, demonstrating that a proper description of the anharmonic motions of the chromophore is not relevant in the computation of the absorption properties. In addition, it is also found that solvent organization is a rather fast process and a long sampling is not required. Finally, it is also demonstrated that the same exchange-correlation functional should be employed in the sampling and in the computation of the excited states properties to avoid unphysical triplet states with relative energies close or below 0 eV
Photoabsorption of Icosahedral Noble Metal Clusters: An Efficient TDDFT Approach to Large-Scale Systems
7noWe apply a recently developed time-dependent density functional theory (TDDFT) algorithm based on the complex dynamical polarizability to calculate the photoabsorption spectrum of the following series of closed-shell icosahedral clusters of increasing size (namely, [M13]5+, [M55]3−, [M147]−, and [M309]3+ with M = Ag, Au), focusing in particular on their plasmonic response. The new method is shown to be computationally very efficient: it simultaneously retains information on the excited-state wave function and provides a detailed analysis of the optical resonances, e.g., by employing the transition contribution map scheme. For silver clusters, a very intense plasmon resonance is found for [Ag55]3−, with strong coupling among low-energy single-particle configurations. At variance, for gold clusters we do not find a single strong plasmonic peak but rather many features of comparable intensity, with partial plasmonic behavior present only for the lowest-energy transitions. Notably, we also find a much greater sensitivity of the optical response of Ag clusters with respect to Au clusters to cluster charge, the exchange-correlation (xc) functional, and the basis set, as demonstrated via a detailed comparison between [Ag55]q and [Au55]q. The results of the TDDFT algorithm obtained with the
complex dynamical polarizability are finally compared with those produced by alternative (real-time evolution or Lanczos) approaches, showing that, upon proper choice of numerical parameters, overall nearly quantitative agreement is achieved among all of the considered approaches, in keeping with their fundamental equivalence.partially_openopenBaseggio, Oscar; De Vetta, Martina; Fronzoni, Giovanna; Stener, Mauro; Sementa, Luca; Fortunelli, Alessandro; Calzolari, ArrigoBaseggio, Oscar; De Vetta, Martina; Fronzoni, Giovanna; Stener, Mauro; Sementa, Luca; Fortunelli, Alessandro; Calzolari, Arrig
Ligand-Enhanced Optical Response of Gold Nanomolecules and Its Fragment Projection Analysis: The Case of Au30(SR)18
8siHere we investigate via first-principles simulations
the optical absorption spectra of three different
Au30(SR)18 monolayer-protected clusters (MPC):
Au30(StBu)18, Au30(SPh)18, and Au30(SPh-pNO2)18.
Au30(StBu)18 is known in the literature, and its crystal structure
is available. In contrast, Au30(SPh)18 and Au30(SPh-pNO2)18
are two species that have been designed by replacing the tertbutyl
organic residues of Au30(StBu)18 with aromatic ones so as
to investigate the effects of ligand replacement on the optical
response of Au nanomolecules. By analogy to a previously
studied Au23(SR)16
− anionic species, despite distinct differences
in charge and chemical composition, a substantial ligand
enhancement of the absorption intensity in the optical region
is also obtained for the Au30(SPh-pNO2)18 MPC. The use of
conjugated aromatic ligands with properly chosen electron-withdrawing substituents and exhibiting steric hindrance so as to also
achieve charge decompression at the surface is therefore demonstrated as a general approach to enhancing the MPC
photoabsorption intensity in the optical region. Additionally, we here subject the ligand-enhancement phenomenon to a detailed
analysis based on the fragment projection of electronic excited states and on induced transition densities, leading to a better
understanding of the physical origin of this phenomenon, thus opening avenues to its more precise control and exploitation.reservedmixedSementa, Luca; Barcaro, Giovanni; Baseggio, Oscar; De Vetta, Martina; Dass, Amala; Aprà, Edoardo; Stener, Mauro; Fortunelli, AlessandroSementa, Luca; Barcaro, Giovanni; Baseggio, Oscar; De Vetta, Martina; Dass, Amala; Aprà, Edoardo; Stener, Mauro; Fortunelli, Alessandr
Ligand-Enhanced Optical Response of Gold Nanomolecules and Its Fragment Projection Analysis: The Case of Au<sub>30</sub>(SR)<sub>18</sub>
Here
we investigate via first-principles simulations the optical
absorption spectra of three different Au<sub>30</sub>(SR)<sub>18</sub> monolayer-protected clusters (MPC): Au<sub>30</sub>(S<sup>t</sup>Bu)<sub>18</sub>, Au<sub>30</sub>(SPh)<sub>18</sub>, and Au<sub>30</sub>(SPh-<i>p</i>NO<sub>2</sub>)<sub>18</sub>. Au<sub>30</sub>(S<sup>t</sup>Bu)<sub>18</sub> is known in the literature, and its
crystal structure is available. In contrast, Au<sub>30</sub>(SPh)<sub>18</sub> and Au<sub>30</sub>(SPh-<i>p</i>NO<sub>2</sub>)<sub>18</sub> are two species that have been designed by replacing
the <i>tert</i>-butyl organic residues of Au<sub>30</sub>(S<sup>t</sup>Bu)<sub>18</sub> with aromatic ones so as to investigate
the effects of ligand replacement on the optical response of Au nanomolecules.
By analogy to a previously studied Au<sub>23</sub>(SR)<sub>16</sub><sup>–</sup> anionic species, despite distinct differences
in charge and chemical composition, a substantial ligand enhancement
of the absorption intensity in the optical region is also obtained
for the Au<sub>30</sub>(SPh-<i>p</i>NO<sub>2</sub>)<sub>18</sub> MPC. The use of conjugated aromatic ligands with properly
chosen electron-withdrawing substituents and exhibiting steric hindrance
so as to also achieve charge decompression at the surface is therefore
demonstrated as a general approach to enhancing the MPC photoabsorption
intensity in the optical region. Additionally, we here subject the
ligand-enhancement phenomenon to a detailed analysis based on the
fragment projection of electronic excited states and on induced transition
densities, leading to a better understanding of the physical origin
of this phenomenon, thus opening avenues to its more precise control
and exploitation